Week 4 : Next Generation Sequencing: techniques and data Introduction to Bioinformatics (LF:DSIB01) Adobe Systems Nucleic Acid Sequencing History 2 Sanger Sequencing Steps & Method Sanger Sequencing – Bacteriophage genome sequenced: 1977 Adobe Systems Nucleic Acid Sequencing History 3 1995 – Shotgun Sequencing Shotgun Sequencing Adobe Systems Nucleic Acid Sequencing History 4 GWAS Catalog on Twitter: "In 2001, #OnThisDay the first Human Genome was published in @nature and tomorrow in @sciencemagazine, so many advances since then and more to come!!… https://t.co/SsaoPYEd0r" 2001 Human Genome Sequenced Cost: ~300M USD Adobe Systems Nucleic Acid (not-)Sequencing History 5 1.9 - Microarrays | STAT 555 Microarray Technology 2000s - Microarrays Adobe Systems Nucleic Acid Sequencing History 6 Illumina (Solexa) sequencing - GENOMICS 2006 – Solexa Genome Analyser 2007 – Solexa bought by Illumina Illumina Genome Analyzer sequencing. Adapter-modified, single-stranded... | Download Scientific Diagram $1,000 genome - Wikipedia Next Generation Sequencing New Generation Sequencing NGS Introduction to the Human Genome 2014 Alexei Fedorov 2015 Adobe Systems NGS Data analysis workflow 7 Today’s Practical Next Lecture + Practical Adapters for Next Generation Sequencing - LubioScience Babraham Bioinformatics - FastQC A Quality Control tool for High Throughput Sequence Data Adobe Systems Long Read Sequencing 8 Pore over this: Advances in DNA sequencing - The Oxford Scientist First Nanopore Sequencing of Human Genome Long Reads – Low per read accuracy Adobe Systems RNA-Seq 9 RNA sequencing: the teenage years | Nature Reviews Genetics RNA-seqlopedia Adobe Systems RNA-Seq Analysis •Alignment to transcriptome or genome (gapped) • •Poly-A selection or Ribosomal RNA depletion • •Can be used to quantify RNA, or to identify structural differences (e.g. splicing) • •Usual downstream analysis: Fold Change between conditions 10 Adobe Systems Immunoprecipitation based techniques 11 Mapping of DNA-protein interaction sites: CHIP seq - France Génomique ChIP-Seq : DNA Binding Proteins Fig. 1 CLIP-Seq : RNA Binding Proteins Adobe Systems 12 Fig. 2 https://www.nature.com/articles/s43586-021-00018-1 Adobe Systems Ribo-Seq 13 Current Research - Biochemistry and Molecular Biology Identification of actively translated RNA Exact position of Ribosome Observing differential translation in GWIPS-viz. Ribo-seq (red) and... | Download Scientific Diagram Adobe Systems ATAC-Seq 14 Mapping of chromatin accessibility sites: ATAC seq - France Génomique Identification of accessible chromatin areas Adobe Systems Shape-Seq 15 The basic SHAPE-Seq protocol. In SHAPE-Seq (6,7), RNAs are modified... | Download Scientific Diagram Adobe Systems … and others 16 Adobe Systems Adobe Systems Adobe Systems Adobe Systems Adobe Systems Adobe Systems 17 www.ceitec.eu CEITEC @CEITEC_Brno >